J4_1VY6_001

3D structure

PDB id

1VY6 (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the Thermus thermophilus 70S ribosome in the pre-attack state of peptide bond formation containing short substrate-mimic Cytidine-Puromycin in the A site and acylated tRNA in the P site.

Experimental method

X-RAY DIFFRACTION

Resolution

2.9 Å

Loop

Sequence

GAGUAACG*UC*GUAG*CC

Length

16 nucleotides

Bulged bases

1VY6|1|AA|C|121

QA status

Valid loop

Sequence variability

If this chain is mapped to an Rfam alignment, the link below will give its sequence variability.

R3DSVS

Structural variability across Equivalence Class

The link below will give the loop's structural variability across the equivalence class for this chain.

R3DMCS EC

Structural variability across Rfam

If this chain is mapped to an Rfam alignment, the link below will give the loop's structural variability between chains mapped to the same Rfam family.

R3DMCS Rfam

J4_1VY6_001 not in the Motif Atlas

Homologous match to J4_4LFB_001

Geometric discrepancy: 0.0924

The information below is about J4_4LFB_001

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_90044.1

Basepair signature

cWW-F-cWW-F-F-F-tHW-F-cWW-cWW

Number of instances in this motif group

2

Unit IDs

1VY6|1|AA|G|115
1VY6|1|AA|A|116
1VY6|1|AA|G|117
1VY6|1|AA|U|118
1VY6|1|AA|A|119
1VY6|1|AA|A|120
1VY6|1|AA|C|121
1VY6|1|AA|G|122
*
1VY6|1|AA|U|239
1VY6|1|AA|C|240
*
1VY6|1|AA|G|286
1VY6|1|AA|U|287
1VY6|1|AA|A|288
1VY6|1|AA|G|289
*
1VY6|1|AA|C|311
1VY6|1|AA|C|312

Current chains

Chain AA

16S Ribosomal RNA

Nearby chains

Chain AP

30S ribosomal protein S16

Chain AQ

30S ribosomal protein S17